It's a perfectly sensible answer. This is no different from a custom game in CivIV when you uncheck diplomatic victory or space race, and can't build the UN or the Apollo Program. It's like that in all Meier games, if you disable a victory condition, you can't do the things that would bring on that victory if you had it checked. (Except I suppose eliminating opponents for conquest.)
I personally leave Independence as the ONLY victory condition checked. That way, you don't have any time limit and can declare independence at leisure.
I also think it might be cool if a future patch had other victory conditions. You should be able to win victory as a loyalist, by building a really big empire, or eliminating all European rivals, or wiping out X% of native settlements/native nations, or whatever. It might be interesting if you could choose whether your Statesmen generated Liberty Bells (towards independence) or Loyalty Bells (same other effects but no increase in rebel sentiment). Of course, to make this work they would have to balance the European AI as well -- right now the natives can be pretty formidable but the Europeans are pushovers.
